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tests/testthat/_snaps/count_occurrences_by_grade.md
In tern: Create Common TLGs Used in Clinical Trials
h_append_grade_groups works with valid input
Code
res
Output
$`Any Grade`
[1] 150
$`Grade 1-2`
[1] 30
$`1`
[1] 10
$`2`
[1] 20
$`Grade 3-4`
[1] 70
$`3`
[1] 30
$`4`
[1] 40
$`5`
[1] 50
h_append_grade_groups works with valid input with revers order and one-element grade groups
Code
res
Output
$`Any Grade`
[1] 150
$`Grade A`
[1] 50
$`Grade B`
[1] 70
$`4`
[1] 40
$`3`
[1] 30
$`2`
[1] 20
$`1`
[1] 10
s_count_occurrences_by_grade works with valid input and default arguments for grade
Code
res
Output
$count_fraction
$count_fraction$`1`
[1] 2.0 0.2
$count_fraction$`2`
[1] 2.0 0.2
$count_fraction$`3`
[1] 2.0 0.2
$count_fraction$`4`
[1] 0 0
$count_fraction$`5`
[1] 0 0
Code
res
Output
$count_fraction
$count_fraction$`1`
[1] 0 0
$count_fraction$`2`
[1] 0 0
$count_fraction$`3`
[1] 0 0
$count_fraction$`4`
[1] 0 0
$count_fraction$`5`
[1] 0 0
s_count_occurrences_by_grade sorts grade levels so that 'missing' level appears last
Code
res
Output
$count_fraction
$count_fraction$`1`
[1] 2.0 0.2
$count_fraction$`2`
[1] 2.0 0.2
$count_fraction$`3`
[1] 1.0 0.1
$count_fraction$`4`
[1] 0 0
$count_fraction$`5`
[1] 0 0
$count_fraction$Missing
[1] 1.0 0.1
s_count_occurrences_by_grade works with valid input for grade grouping
Code
res
Output
$count_fraction
$count_fraction$`Any Grade`
[1] 6.0 0.6
$count_fraction$`Grade 1-2`
[1] 4.0 0.4
$count_fraction$`1`
[1] 2.0 0.2
$count_fraction$`2`
[1] 2.0 0.2
$count_fraction$`Grade 3-4`
[1] 2.0 0.2
$count_fraction$`3`
[1] 2.0 0.2
$count_fraction$`4`
[1] 0 0
$count_fraction$`5`
[1] 0 0
Code
res
Output
$count_fraction
$count_fraction$`Any Grade`
[1] 0 0
$count_fraction$`Grade 1-2`
[1] 0 0
$count_fraction$`1`
[1] 0 0
$count_fraction$`2`
[1] 0 0
$count_fraction$`Grade 3-4`
[1] 0 0
$count_fraction$`3`
[1] 0 0
$count_fraction$`4`
[1] 0 0
$count_fraction$`5`
[1] 0 0
Code
res
Output
$count_fraction
$count_fraction$`Any Grade`
[1] 6.0 0.6
$count_fraction$`Grade 1-2`
[1] 4.0 0.4
$count_fraction$`Grade 3-4`
[1] 2.0 0.2
s_count_occurrences_by_grade works with valid input for intensity and custom arguments
Code
res
Output
$count_fraction
$count_fraction$`Any Intensity`
[1] 6.0 0.6
$count_fraction$MILD
[1] 2.0 0.2
$count_fraction$MODERATE
[1] 2.0 0.2
$count_fraction$SEVERE
[1] 2.0 0.2
count_occurrences_by_grade works with default arguments for intensity
Code
res
Output
A B
(N=3) (N=3)
————————————————————————————————
MILD 0 2 (66.7%)
MODERATE 1 (33.3%) 1 (33.3%)
SEVERE 2 (66.7%) 0
Code
res
Output
A B D
(N=3) (N=3) (N=0)
————————————————————————————————————————
MILD 0 2 (66.7%) NA
MODERATE 1 (33.3%) 1 (33.3%) NA
SEVERE 2 (66.7%) 0 NA
count_occurrences_by_grade label works when more than one variables are analyzed
Code
res
Output
A B
(N=3) (N=3)
——————————————————————————————————————
AESEV
MILD 0 2 (66.7%)
MODERATE 1 (33.3%) 1 (33.3%)
SEVERE 2 (66.7%) 0
Toxicity Grade
1 0 2 (66.7%)
2 1 (33.3%) 1 (33.3%)
3 2 (66.7%) 0
4 0 0
5 0 0
count_occurrences_by_grade works with custom arguments for grade
Code
res
Output
A B
(N=3) (N=3)
———————————————————————————————————————————
-Any- 3.00 (100.00%) 3.00 (100.00%)
Grade 1-2 1.00 (33.33%) 3.00 (100.00%)
1 0.00 (0.00%) 2.00 (66.67%)
2 1.00 (33.33%) 1.00 (33.33%)
Grade 3-5 2.00 (66.67%) 0.00 (0.00%)
3 2.00 (66.67%) 0.00 (0.00%)
4 0.00 (0.00%) 0.00 (0.00%)
5 0.00 (0.00%) 0.00 (0.00%)
Code
res
Output
A B
(N=3) (N=3)
———————————————————————————————————————————
-Any- 3.00 (100.00%) 3.00 (100.00%)
Grade 1-2 1.00 (33.33%) 3.00 (100.00%)
Grade 3-5 2.00 (66.67%) 0.00 (0.00%)
summarize_occurrences_by_grade works with default arguments for intensity
Code
res
Output
all obs
(N=9)
——————————————————————————
A
MILD 0.00 (0.00%)
MODERATE 1.00 (11.11%)
SEVERE 2.00 (22.22%)
B
MILD 2.00 (22.22%)
MODERATE 1.00 (11.11%)
SEVERE 0.00 (0.00%)
Code
res
Output
A B D
(N=10) (N=10) (N=0)
———————————————————————————————————————————————————————
LOW
MILD 0.00 (0.00%) 1.00 (10.00%) 0.00 (NA%)
MODERATE 0.00 (0.00%) 0.00 (0.00%) 0.00 (NA%)
SEVERE 2.00 (20.00%) 0.00 (0.00%) 0.00 (NA%)
HIGH
MILD 0.00 (0.00%) 1.00 (10.00%) 0.00 (NA%)
MODERATE 1.00 (10.00%) 1.00 (10.00%) 0.00 (NA%)
SEVERE 0.00 (0.00%) 0.00 (0.00%) 0.00 (NA%)
summarize_occurrences_by_grade works with custom arguments for grade
Code
res
Output
all obs
(N=10)
———————————————————————
A
-Any- 3 (30.0%)
Grade 1-2 1 (10.0%)
1 0
2 1 (10.0%)
Grade 3-5 2 (20.0%)
3 2 (20.0%)
4 0
5 0
B
-Any- 3 (30.0%)
Grade 1-2 3 (30.0%)
1 2 (20.0%)
2 1 (10.0%)
Grade 3-5 0
3 0
4 0
5 0
count_occurrences_by_grade works with trim_levels_in_group split function
Code
res
Output
ARM A ARM B
(N=15) (N=15)
————————————————————————————————————
SOC1
-Any- 15 (100%) 15 (100%)
Grade 1-2 15 (100%) 15 (100%)
1 10 (66.7%) 0
2 5 (33.3%) 15 (100%)
count_occurrences_by_grade works as expected with risk difference column
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
——————————————————————————————————————————————————————————————————————————————————
MILD 6 (3.0%) 4 (2.3%) 2 (1.2%) 0.7 (-2.5 - 3.9)
MODERATE 19 (9.4%) 15 (8.5%) 14 (8.6%) 0.9 (-4.8 - 6.7)
SEVERE 34 (16.8%) 38 (21.5%) 32 (19.8%) -4.6 (-12.6 - 3.3)
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
————————————————————————————————————————————————————————————————————————————————————
-Any- 25 (12.4%) 34 (19.2%) 28 (17.3%) -6.8 (-14.2 - 0.5)
MILD 1 (0.5%) 2 (1.1%) 0 -0.6 (-2.5 - 1.2)
MODERATE 7 (3.5%) 9 (5.1%) 6 (3.7%) -1.6 (-5.7 - 2.5)
SEVERE 17 (8.4%) 23 (13.0%) 22 (13.6%) -4.6 (-10.8 - 1.7)
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h_append_grade_groups works with valid input
Code
res
Output
$`Any Grade`
[1] 150
$`Grade 1-2`
[1] 30
$`1`
[1] 10
$`2`
[1] 20
$`Grade 3-4`
[1] 70
$`3`
[1] 30
$`4`
[1] 40
$`5`
[1] 50
h_append_grade_groups works with valid input with revers order and one-element grade groups
Code
res
Output
$`Any Grade`
[1] 150
$`Grade A`
[1] 50
$`Grade B`
[1] 70
$`4`
[1] 40
$`3`
[1] 30
$`2`
[1] 20
$`1`
[1] 10
s_count_occurrences_by_grade works with valid input and default arguments for grade
Code
res
Output
$count_fraction
$count_fraction$`1`
[1] 2.0 0.2
$count_fraction$`2`
[1] 2.0 0.2
$count_fraction$`3`
[1] 2.0 0.2
$count_fraction$`4`
[1] 0 0
$count_fraction$`5`
[1] 0 0
Code
res
Output
$count_fraction
$count_fraction$`1`
[1] 0 0
$count_fraction$`2`
[1] 0 0
$count_fraction$`3`
[1] 0 0
$count_fraction$`4`
[1] 0 0
$count_fraction$`5`
[1] 0 0
s_count_occurrences_by_grade sorts grade levels so that 'missing' level appears last
Code
res
Output
$count_fraction
$count_fraction$`1`
[1] 2.0 0.2
$count_fraction$`2`
[1] 2.0 0.2
$count_fraction$`3`
[1] 1.0 0.1
$count_fraction$`4`
[1] 0 0
$count_fraction$`5`
[1] 0 0
$count_fraction$Missing
[1] 1.0 0.1
s_count_occurrences_by_grade works with valid input for grade grouping
Code
res
Output
$count_fraction
$count_fraction$`Any Grade`
[1] 6.0 0.6
$count_fraction$`Grade 1-2`
[1] 4.0 0.4
$count_fraction$`1`
[1] 2.0 0.2
$count_fraction$`2`
[1] 2.0 0.2
$count_fraction$`Grade 3-4`
[1] 2.0 0.2
$count_fraction$`3`
[1] 2.0 0.2
$count_fraction$`4`
[1] 0 0
$count_fraction$`5`
[1] 0 0
Code
res
Output
$count_fraction
$count_fraction$`Any Grade`
[1] 0 0
$count_fraction$`Grade 1-2`
[1] 0 0
$count_fraction$`1`
[1] 0 0
$count_fraction$`2`
[1] 0 0
$count_fraction$`Grade 3-4`
[1] 0 0
$count_fraction$`3`
[1] 0 0
$count_fraction$`4`
[1] 0 0
$count_fraction$`5`
[1] 0 0
Code
res
Output
$count_fraction
$count_fraction$`Any Grade`
[1] 6.0 0.6
$count_fraction$`Grade 1-2`
[1] 4.0 0.4
$count_fraction$`Grade 3-4`
[1] 2.0 0.2
s_count_occurrences_by_grade works with valid input for intensity and custom arguments
Code
res
Output
$count_fraction
$count_fraction$`Any Intensity`
[1] 6.0 0.6
$count_fraction$MILD
[1] 2.0 0.2
$count_fraction$MODERATE
[1] 2.0 0.2
$count_fraction$SEVERE
[1] 2.0 0.2
count_occurrences_by_grade works with default arguments for intensity
Code
res
Output
A B
(N=3) (N=3)
————————————————————————————————
MILD 0 2 (66.7%)
MODERATE 1 (33.3%) 1 (33.3%)
SEVERE 2 (66.7%) 0
Code
res
Output
A B D
(N=3) (N=3) (N=0)
————————————————————————————————————————
MILD 0 2 (66.7%) NA
MODERATE 1 (33.3%) 1 (33.3%) NA
SEVERE 2 (66.7%) 0 NA
count_occurrences_by_grade label works when more than one variables are analyzed
Code
res
Output
A B
(N=3) (N=3)
——————————————————————————————————————
AESEV
MILD 0 2 (66.7%)
MODERATE 1 (33.3%) 1 (33.3%)
SEVERE 2 (66.7%) 0
Toxicity Grade
1 0 2 (66.7%)
2 1 (33.3%) 1 (33.3%)
3 2 (66.7%) 0
4 0 0
5 0 0
count_occurrences_by_grade works with custom arguments for grade
Code
res
Output
A B
(N=3) (N=3)
———————————————————————————————————————————
-Any- 3.00 (100.00%) 3.00 (100.00%)
Grade 1-2 1.00 (33.33%) 3.00 (100.00%)
1 0.00 (0.00%) 2.00 (66.67%)
2 1.00 (33.33%) 1.00 (33.33%)
Grade 3-5 2.00 (66.67%) 0.00 (0.00%)
3 2.00 (66.67%) 0.00 (0.00%)
4 0.00 (0.00%) 0.00 (0.00%)
5 0.00 (0.00%) 0.00 (0.00%)
Code
res
Output
A B
(N=3) (N=3)
———————————————————————————————————————————
-Any- 3.00 (100.00%) 3.00 (100.00%)
Grade 1-2 1.00 (33.33%) 3.00 (100.00%)
Grade 3-5 2.00 (66.67%) 0.00 (0.00%)
summarize_occurrences_by_grade works with default arguments for intensity
Code
res
Output
all obs
(N=9)
——————————————————————————
A
MILD 0.00 (0.00%)
MODERATE 1.00 (11.11%)
SEVERE 2.00 (22.22%)
B
MILD 2.00 (22.22%)
MODERATE 1.00 (11.11%)
SEVERE 0.00 (0.00%)
Code
res
Output
A B D
(N=10) (N=10) (N=0)
———————————————————————————————————————————————————————
LOW
MILD 0.00 (0.00%) 1.00 (10.00%) 0.00 (NA%)
MODERATE 0.00 (0.00%) 0.00 (0.00%) 0.00 (NA%)
SEVERE 2.00 (20.00%) 0.00 (0.00%) 0.00 (NA%)
HIGH
MILD 0.00 (0.00%) 1.00 (10.00%) 0.00 (NA%)
MODERATE 1.00 (10.00%) 1.00 (10.00%) 0.00 (NA%)
SEVERE 0.00 (0.00%) 0.00 (0.00%) 0.00 (NA%)
summarize_occurrences_by_grade works with custom arguments for grade
Code
res
Output
all obs
(N=10)
———————————————————————
A
-Any- 3 (30.0%)
Grade 1-2 1 (10.0%)
1 0
2 1 (10.0%)
Grade 3-5 2 (20.0%)
3 2 (20.0%)
4 0
5 0
B
-Any- 3 (30.0%)
Grade 1-2 3 (30.0%)
1 2 (20.0%)
2 1 (10.0%)
Grade 3-5 0
3 0
4 0
5 0
count_occurrences_by_grade works with trim_levels_in_group split function
Code
res
Output
ARM A ARM B
(N=15) (N=15)
————————————————————————————————————
SOC1
-Any- 15 (100%) 15 (100%)
Grade 1-2 15 (100%) 15 (100%)
1 10 (66.7%) 0
2 5 (33.3%) 15 (100%)
count_occurrences_by_grade works as expected with risk difference column
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
——————————————————————————————————————————————————————————————————————————————————
MILD 6 (3.0%) 4 (2.3%) 2 (1.2%) 0.7 (-2.5 - 3.9)
MODERATE 19 (9.4%) 15 (8.5%) 14 (8.6%) 0.9 (-4.8 - 6.7)
SEVERE 34 (16.8%) 38 (21.5%) 32 (19.8%) -4.6 (-12.6 - 3.3)
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
————————————————————————————————————————————————————————————————————————————————————
-Any- 25 (12.4%) 34 (19.2%) 28 (17.3%) -6.8 (-14.2 - 0.5)
MILD 1 (0.5%) 2 (1.1%) 0 -0.6 (-2.5 - 1.2)
MODERATE 7 (3.5%) 9 (5.1%) 6 (3.7%) -1.6 (-5.7 - 2.5)
SEVERE 17 (8.4%) 23 (13.0%) 22 (13.6%) -4.6 (-10.8 - 1.7)
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